The excessive use of plastics has been accompanied by severe ecologically damaging effects. The recent discovery of a PETase from Ideonella sakaiensis that decomposes poly(ethylene terephthalate) (PET) under mild conditions provides an attractive avenue for the biodegradation of plastics. However, the inherent instability of the enzyme limits its practical utilization. Here, we devised a novel computational strategy (greedy accumulated strategy for protein engineering, GRAPE). A systematic clustering analysis combined with greedy accumulation of beneficial mutations in a computationally derived library enabled the design of a variant, DuraPETase, which exhibits an apparent melting temperature that is drastically elevated by 31C and strikingly enhanced degradation performance toward semicrystalline PET films (23%) at mild temperatures (over two orders of magnitude improvement). The mechanism underlying the robust promotion of enzyme performance has been demonstrated via a crystal structure and molecular dynamics simulations. This work shows the capabilities of computational enzyme design to circumvent antagonistic epistatic effects and provides a valuable tool for further understanding and advancing polyester hydrolysis in the natural environment
Development of potent biocatalysts for enzymatic detoxification of estrogenic mycotoxin zearalenone (ZEN) and its more toxic derivative alpha-zearalenol (alpha-ZOL) is of great interest. Here, we report the crystal structures of a ZEN-hydrolyzing enzyme from Rhinocladiella mackenziei (RmZHD), including substrate complexes. A molecular mechanism for the distinct activity of RmZHD in hydrolyzing the structurally similar ZEN and alpha-ZOL is then proposed. In addition, structure-based engineering to modify the substrate-binding pocket and improve the RmZHD activity toward alpha-ZOL is presented. These results expand our scope in understanding the catalytic mechanism of ZHD-family enzymes and are of vital importance in further industrial applications.
